If you have a keyboard...
ALT+F4 will close apps or programs....including a browser with a frozen popup whether in Desktop or Metro/Modern/Start screen

If you don't have a keyboard and are using Touch screen....
If at Desktop screen...
Open Task Manager...via long hold(right click equivalent) on Windows icon on task bar(lower left)...or long hold(right click equivalent) on Taskbar...select 'Task Manager'.
In Processes tab, select desired program (eg IE/Chrome/Firefox or other open program). select 'End Task' (lower right corner)

If at Start/Metro/Modern screen...
Swipe right(from left side of screen) part way until Desktop enlarges to half the screen and browser/app is the other half...then swipe down on browser/app to bottom of screen to close it.

If you suspect a malware popup, then running your antivirus software, CCleaner and Malwarebytes could be a good option to remove anything that might have gained traction.